Merge 6ae1b46 into bcea95d

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "2.4.7"
+version = "2.4.8"
 description = "Clinical Genomics Analysis Platform"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

src/encoded/tests/test_util.py

@@ -7,7 +7,7 @@
 from unittest import mock
 from dcicutils.qa_utils import ControlledTime
 from ..util import (
-    debuglog, deduplicate_list, gunzip_content, resolve_file_path, ENCODED_ROOT_DIR, generate_fastq_file,
+    debuglog, deduplicate_list, gunzip_content, resolve_file_path, ENCODED_ROOT_DIR,
 )
 from .. import util as util_module
 
@@ -231,7 +231,3 @@ def log_content():
             os.remove(filename)
         except Exception:
             pass
-
-
-# def test_generate_fastq_file():
-#     ... Need test of generate_fastq_file here ...

src/encoded/types/cohort.py

@@ -15,7 +15,8 @@
 from snovault.util import debug_log
 from webtest import TestApp
 from xml.etree.ElementTree import fromstring
-from .base import Item, get_item_or_none
+from .base import Item
+from ..util import get_trusted_email
 
 
 log = structlog.getLogger(__name__)
@@ -115,17 +116,7 @@ def process_pedigree(context, request):
     ped_timestamp = ped_datetime.isoformat() + '+00:00'
     app = get_app(config_uri, 'app')
     # get user email for TestApp authentication
-    email = getattr(request, '_auth0_authenticated', None)
-    if not email:
-        user_uuid = None
-        for principal in request.effective_principals:
-            if principal.startswith('userid.'):
-                user_uuid = principal[7:]
-                break
-        if not user_uuid:
-            raise HTTPUnprocessableEntity('Cohort %s: Must provide authentication' % cohort)
-        user_props = get_item_or_none(request, user_uuid)
-        email = user_props['email']
+    email = get_trusted_email(request, context="Cohort %s" % cohort)
     environ = {'HTTP_ACCEPT': 'application/json', 'REMOTE_USER': email}
     testapp = TestApp(app, environ)
 

src/encoded/types/family.py

@@ -19,6 +19,7 @@
 from webtest import TestApp
 from xml.etree.ElementTree import fromstring
 from .base import Item, get_item_or_none
+from ..util import get_trusted_email
 
 
 log = structlog.getLogger(__name__)
@@ -598,17 +599,7 @@ def process_pedigree(context, request):
     ped_timestamp = ped_datetime.isoformat() + '+00:00'
     app = get_app(config_uri, 'app')
     # get user email for TestApp authentication
-    email = getattr(request, '_auth0_authenticated', None)
-    if not email:
-        user_uuid = None
-        for principal in request.effective_principals:
-            if principal.startswith('userid.'):
-                user_uuid = principal[7:]
-                break
-        if not user_uuid:
-            raise HTTPUnprocessableEntity('Family %s: Must provide authentication' % family_item)
-        user_props = get_item_or_none(request, user_uuid)
-        email = user_props['email']
+    email = get_trusted_email(request, context="Family %s" % family_item)
     environ = {'HTTP_ACCEPT': 'application/json', 'REMOTE_USER': email}
     testapp = TestApp(app, environ)
 

src/encoded/util.py

@@ -3,17 +3,17 @@
 import gzip
 import io
 import os
-import random
 import pyramid.request
 import tempfile
 
 from dcicutils.misc_utils import check_true
 from io import BytesIO
+from pyramid.httpexceptions import HTTPUnprocessableEntity
 from snovault import COLLECTIONS, Collection
 from snovault.crud_views import collection_add as sno_collection_add
 from snovault.embed import make_subrequest
 from snovault.schema_utils import validate_request
-from typing import Type
+from .types.base import get_item_or_none
 
 
 ENCODED_ROOT_DIR = os.path.dirname(__file__)
@@ -238,38 +238,35 @@ def create_empty_s3_file(s3_client, bucket: str, key: str):
     s3_client.upload_file(empty_file, Bucket=bucket, Key=key)
 
 
-def generate_fastq_file(filename, num=10, length=10):
+def get_trusted_email(request, context=None, raise_errors=True):
     """
-    Creates a new fastq file with the given name, containing (pseudo)randomly generated content.
+    Get an email address on behalf of which we can issue other requests.
 
-    Example usage:
-
-        fastq_generator('fastq_sample.fastq.gz', 25, 50)
-           creates a new fastq file with 25 sequences, each of length 50.
-
-        fastq_generator('fastq_sample.fastq.gz')
-           creates a new fastq file with default characteristics (10 sequences, each of length 10).
-
-    Args:
-        filename str: the name of a file to create
-        num int: the number of random sequences (default 10)
-        length int: the length of the random sequences (default 10)
-
-    Returns:
-        the filename
+    If auth0 has authenticated user info to offer, return that.
+    Otherwise, look for a userid.xxx among request.effective_principals and get the email from that.
 
+    This will raise HTTPUnprocessableEntity if there's a problem obtaining the mail.
     """
-    if not filename.endswith('.fastq.gz'):
-        filename = filename.rstrip('fastq').rstrip('fq').rstrip('.') + '.fastq.gz'
-    content = ''
-    bases = 'ACTG'
-
-    for i in range(num):
-        content += '@SEQUENCE{} length={}\n'.format(i, length)
-        content += ''.join(random.choice(bases) for i in range(length)) + '\n'
-        content += '+\n'
-        content += 'I' * length + '\n'
-    with gzip.open(filename, 'w') as outfile:
-        outfile.write(content.encode('ascii'))
-
-    return filename
+    try:
+        # import pdb;pdb.set_trace()
+        context = context or "Requirement"
+        email = getattr(request, '_auth0_authenticated', None)
+        if not email:
+            user_uuid = None
+            for principal in request.effective_principals:
+                if principal.startswith('userid.'):
+                    user_uuid = principal[7:]
+                    break
+            if not user_uuid:
+                raise HTTPUnprocessableEntity('%s: Must provide authentication' % context)
+            user_props = get_item_or_none(request, user_uuid)
+            if not user_props:
+                raise HTTPUnprocessableEntity('%s: User profile missing' % context)
+            if 'email' not in user_props:
+                raise HTTPUnprocessableEntity('%s: Entry for "email" missing in user profile.' % context)
+            email = user_props['email']
+        return email
+    except Exception:
+        if raise_errors:
+            raise
+        return None